War aganist Hydra
by Supreme Commander
Summary: After the Fall of S.H.I.E.L.D. Phil Colson begins rebuilding from scratch I'm recruited to join the New Shield. I'm not like your average agent I'm what most people would classify as a super-soldier but my loyalties are to Shield and to humanity. we wage war against the Terrorist Organization known as Hydra with the help of Captain America and the other Avengers.
1. Intro

**Disclaimer: Agents of S.H.I.E.L.D or any of Marvel stuff doesn't belong to me.**

 **Author Note: This is my version of Agents of Shield my character joins Phil Coulson's team after the fall of S.H.I.E.L.D**

 **Intro**

My name is Agent 118 but my real name is John Horton I'm an Agent of S.H.I.E.L.D. I've been an agent since Director Nick Fury recruited me after I encountered Hydra when I was in Delta Force. I grew up in an orphanage for as long as I could remember before that is blank. I was never adopted. After high school I did manage to get to college since I had very good grades throughout school. Once I enter college I found out I wanted to join the military so I go through Army ROTC at the school. After graduating I became a foot soldier but I eventually land in Delta. . I remember arriving at S.H.I.E.L.D Academy making several friends some who would turned out to be Hydra Agents. I graduated from the academy and received high marks of course Nick Fury took interest in me. My Supervising Officer after I graduated was Jerry Griffin. We went on several missions together and on one of those I saw him execute innocent civilians of course he wasn't alone he was surrounded by soldiers I never seen before but I knew there weren't Shield agents. I hear him say, "Hail Hydra!" that triggered some flashbacks my parent's death, the parents that took me in and me killing them. I come out. The Hydra soldiers' turned their weapons towards me but Jerry Griffin turns to me. He tries to convince me to join Hydra. I refuse. The Hydra soldiers open fire but their rounds never made contact. Their weapons break apart. I sent their own bullets back to them. Jerry looks at me. He backs away from me but I'm too fast for him I grab him by the throat and looked into his eyes. "What are you?" he asks before I broke his neck.

"I don't know," I reply at his lifeless corpse. I haven't used my powers since the family who took me in when I found out they were with Hydra. I reported to Nick Fury upon my return. I told him the truth. He sits their watching me.

"I knew you father Agent 118 he was a very good agent and one of my best friends. Your father confined in me about your mother after he discovered her secret during a mission. Your mother was also an Agent of Shield. She never told us why she came to Earth."

"What do you mean by us?"

"Your father and me, she saved both of our lives and earn my trust that day and your fathers."

"I have something for you. In the event of their deaths I was supposed to give you this." He give me a locket. "Inside you may find the answers you seek," he tells me.

"I want you to learn to control your abilities your mother had many no telling which ones you have."

"You're not going to Index me?"

"You've been in the Index," he says. "Good luck return when you're ready." I leave his office and head to the Canadian Wilderness to begin training and to find out more about my parents. I knew a little because the director gave me his name but as for my mother's there was nothing. I'm sure the director is keeping some secrets from me but I'm sure of one thing he's not Hydra. He may not have taken my warning that Hydra might have infiltrated S.H.I.E.L.D. but I know they have and I'm safer away just in case Hydra finds out about me.

Three years later I return to SH.I.E.L.D I learned a lot I found a disc inside of the locket which explain lots to me. My mother was from another planet but she never says from where or why she came to Earth but she did say her people are older than the Asgardians. Hydra found the house I was living in when I was 4 they killed both of my parents but I don't remember why I was spared. I found something which says Operation Black Eden but I have no clue I checked shield database but find nothing. It also has coordinates. I plan to check the coordinates out. I heard about the attack on New York I was surprise Nick Fury didn't asks me to join the Avengers. I arrived at Supreme S.H.I. Headquarters in Washington DC. I had to await for the director to see me. After I've been there for forty-five minutes I'm showed into the director's office. "Have a seat," Nick says. "We have somethings to discuss but not here." He writes on a piece of paper and hands it to me. I get up and leave his office.

Hours later we meet at a dinner. "You were right Hydra has infiltrated Shield. I don't know who to trust but your one of the people I trust. I'm not sure how far Hydra has infiltrated but I need your help."

"What can I help with?"

"I need you to head to Site B located in the Nevada Mountains and make sure a facility is secured. Promise me you will help S.H.I.E.L.D survive."

"You have my word Shield will survive," I reply. I leave the dinner first I look over my shoulder and noticed I'm being followed. I enter an alleyway. Three men appear.

"What did Fury want?" One of them asks me. I looked at each of them. I read their minds.

"Stupid Hydra," I said.

"What did you say?" one of them asks.

"I said I hate Hydra." They open fire but I disappeared.

"Where did he go?" another asks.

"Oh boys," I said behind them. I have two pistol in both of my hands. I shoot each of them dead. I disappeared meaning I teleported to Site B. I arrived at Site B. I use my ID card to gain access. The computer system says Welcome Agent Horton security clearance level 8. I entered and is automatically surrounded by agents. I show them my badge and tell them Fury sent me. They lower their weapons and I'm given a tour of the facility. "What is this place?"

"This is a storage facility some of it dates back during War World 2." I still wonder why Fury would send me to a storage facility. "What's your name?"

"John Horton," I answered.

"The CO would like to meet you." I'm escorted to the CO's office. I see a Hydra Flag in the background. I go for my sidearm but I'm hit upside the head. I'm cuffed to the chair in front of the CO's office chair.

"Why did Fury send you here?" the CO asks me.

"No idea I was shocked by his posting," I answered. I'm slapped across the face. "I have no clue why Fury sent me here." I'm slapped again. "Tell your henchmen if he slapped me again I'm going to break his fucking neck." The CO and the others laugh. I'm slapped again. I break the handcuffs. I grabbed the man who kept slapping me and draw his 9mm pistol and killed the other guards. I turned the pistol onto the CO. I use my other hand and snapped the last guard with no effort. I put a bullet into the commanding officer's head. I grab more ammo and another pistol from the dead. I exit the office. Three more guards are coming down the hallway. I pop out and they open fire. I duck back behind cover. I take a breath. Time slowed. I pop out and fire. Time unfreeze and they fall down their bullets missed me. I enter the command center. The few Hydra soldiers left turned towards me but they just vaporized into nothing. I lock down the facility. I look through the facility to try to find any surviving S.H.I.E.L.D Agents but find only bodies. I return to the command center. Turned on the news. I watched as S.H.I.E.L.D. falls from the efforts of Hydra and the destruction of the Hellacarriers in Washington DC.

 **I hope you enjoyed this Intro to this story. Please Read, Review, Favorite, and Follow.**


	2. Chapter 1

**Disclaimer: Agents of Shield or the Avengers or any of the Marvel Comic Book characters doesn't belong to me.**

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Chapter One

Three days after the fall of S.H.I.E.L.D.

I've been in the facility for three days now S.H.I.E.L.D has fallen. I see the news about the events in Washington DC where Captain America save the world form Hydra again. I've never met Steve Rogers but I've heard the stories. They say Director Nick Fury is dead but I doubt that. All of sudden on the screen I see the words scroll across saying Security Breech. I grab an M4 Assault Rifle and head to the entrance. The door is breeched a flashbang is thrown in, but I ducked into the office. The flashbang detonates but it pearly affects me it hurts my ears but that's it. I ling out from behind my cover aiming down the red dot site and waited. Hydra soldiers enter I shoot the first three in the head. I fall back after taking out two more. I hurried to the command center. I enter a code for the self-destruct gather what items I can carry such as a couple of disc Fury told me not to let Hydra get their hands on. Before I can get out of the command center Hydra soldiers open fire. I duck. I pull out a flashbang and throw it. The flashbang disorients the Hydra soldiers I open fire on them dropping six before my M4 jammed. I drop the gun and head towards the back exit. Additional Hydra soldiers arrive and I fire on them with my M1911. I'm hit a couple of times but I keep running. I throw a fragmentation grenade over my shoulder but didn't stick around to find out the results. I slide down a railing. Several S.H.I.E.L.D. vehicles are in the garage. Two Hydra soldiers appeared, I'm hit twice from their P90s but I shoot each of them each in the head. I get into the vehicle. I start the vehicle just as more Hydra soldiers enter. They open fire but had no effect. I open up the car doors and drive out. The Hydra soldiers get into other vehicles and chase after me. The mountain roads can be striking especially with the curves. However two Apache Gunships appeared and open fire. "Fuck can I ever get a break. What do I have that Hydra wants so bad there is no way they know I'm a super-soldier." I pressed a button.

"Defensive and Offensive systems activated."

"Good now I got a spy car," I said. I pressed a button and a missile destroys one of the pursuing SUVs. However the pursuing SUVs a Minigun appears on top of one of them and some sort of cannon on the other. The Apache Gunships are also firing. I look at the Armor 45%. I pressed a button and my own Minigun appeared destroying one of the Attack Choppers. The second Apache fires a missile and it caused me to go off the road and off a cliff. I manage to jump out but I still continue to roll down hitting trees, rocks, and bushes. The SUVs stooped and Hydra soldiers get out.

"No one could survive that?" One Hydra soldiers says.

"We have orders from the Baron to retrieve the data which I'm sure he had on the base is gone along with a dozen of our agents. Contact command tell them to send some reinforcements." A Hydra Sergeant says. They head down to the crash.

I awake my head is pounding. The bullets are still inside of me but I notice the scratches are beginning to heal themselves. My bulletproof vest stopped some of the bullets especially when I took a few rounds to my back. I take out my combat knife if I can heal then if I get the bullet out it should heal itself. I also take out my cell phone it's a phone shield design it as an x-ray function so agents can save lives in the field. I use it on my. The bullets only went a few inches into my body. I grab my small medical kit and remove tweezer from it. I insert the tweezer over the hole where the bullet entered. I insert the tip of the tweezer into the wound. I let out scream removing the bullet hurt like a bitch but as soon as I removed it the wound closes itself. I remove the other bullets screaming each time. I only have my sidearm and a couple of throwing knives. My mission is to escape from Hydra with the disc and not let them fall into their hands. My only chance is to make it to an S.H.I.E.L.D safe house but they could all be compromise by Hydra now. "Why don't you just teleport." I said to myself. "You can kill these Hydra Agents fast you're a super-soldier." All of sudden, I hear a twig snapped and see a person in shield uniform standing behind me and I aimed my pistol at them. "identy yourself there are Hydra Agents around here."

"Agent Backlot," the newcomer answers. The name sounded familiar. "Who are you?"

"Agent Horton," I reply. I lower my weapon. Agent Backlot looks at me and opens fire with his two SMGs. I move out of the way one bullet craze my leg.

"You shouldn't be so quick to trust," he says mocking me. I return fire empting the magazine into his chest but they didn't faze him. He laughs. "I'm a super-soldier of Hydra I have advance healing."

"We'll see about that after I stick a knife in the back of your head," I reply. He discards his SMGs. He reaches behind his back and brings out a M60 LMG. He opens fire. However the projectiles never made it they're stooped just as they came out of his weapon.

"Impressive you're an Inhuman like me, we should be working together."

"Yeah no thinks, I'm an Agent of S.H.I.E.L.D. I wouldn't join Hydra even if Hell freezes over." I notice a smile appears on his face. He fires but once again I stop them. All of sudden his M60 breaks in a thousand pieces. I move so fast and I stick my knife behind his head. "I told you I would stick my knife into your neck." Three Hydra soldiers appeared. They open fire but I deploy a force shield.

"He's an Inhuman," one says. I move so fast they couldn't keep up. I break both of their necks and then I teleport away.

I arrive at the old house I grew up in. I have my M1911 at the ready along with a knife underneath the gun. I kick open the door. They place has been abandon for years. I look around. I head to the study it looks like it was ransacked many years ago but it doesn't look like they found what they were looking for. I sit down at the desk. I begin searching. I find an imprint that looks just like the locket I insert it. All of sudden the bookcase departs revealing a heavy steel door. I go over to it. I see an eye scanner. I look into it. "ID confirm John Horton welcome." A voice says just as the door open. I enter and it closes behind me. I place the locket into another thing.

"John, if you're seeing this it means your mother and I are dead. We loved you very much. I place my trust in the wrong person but it wasn't Nick Fury he's the one you can trust. He has several disc which hold things about Hydra important stuff during when I was under covered. The files are encrypted but I'm sure you can figure them out. You must bring down Hydra or the world is doom, I failed in my attempt to bring the organization down. This house has strict security measures but since I'm dead they weren't activated. Help S.H.I.E.L.D defeat Hydra. Protect the Earth." The message ends. I looked at the disc.

"So these are my father's life work he was trying to bring down Hydra from within their organization and paid with his life and the life of my mother, but why do I have this feeling there is more to this than meets the eye."

Three hours later additional Hydra agents arrive at the location. One of them goes over to Agent Backlot and remove the knife. The wound closes.

"Sir, he was an Inhuman or a super-soldier," Agent Backlot says to one of the Hydra soldiers who apparently is the leader.

"I know Agent Backlot, he's has many powers this is just the Tip of the Spear."

"How do you know Necromancer?" Backlot asks.

"Because he's my son," the Necromancer replies.

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 **I hope you enjoy Chapter 1. I like to think Grazy-Man for the review and those who favorite and follow the story for their support. Feel Free to PM me if you have any suggestions or questions. I will not reveal everything at once. I can tell you the next chapter he's going to join Colson's team. I hope to find a Beta-Reader for this story**


	3. Chapter 2

Chapter Two

I've been at the house I was brought up in for 2 days now going over the stuff my father had on Hydra Secret bases some of them S.H.I.E.L.D facilities. I notice names of Hydra leaders or should I say the heads of Hydra. I remember in Greek Myology which I took in College Hercules son of Zeus fought a Hydra and killed it. Some stuff I couldn't access it was password protected. The heads of Hydra are: Wolfgang Von Strucker, Octavian Bloom, David Whitehall, The Banker, The Baroness, Sheikh, and Doctor List. It has pictures of a few but most didn't have any. All of sudden I hear a knock on the door. I grab my pistol off the table. I shut down the computers. I looked out the eye hole in the door and see two people one in a suit and a hot brunette standing next to him. I hear a footstep behind me. I turned around and has my weapon kicked out of my hands. I knew I could kill her easily but I recognized her as an S.H.I.E.L.D Agent Melinda May. We begin fighting each other. I knew she a very good fighter she was my SO for a little while in the end I manage to get a choke hold one her but that is when Agent Phil Coulson and the hot girl ended. He pointed a weapon at me. I let her go. She looked at me and then at Coulson. "I've see your skills have improved Agent Horton."

"You're still as good as ever Agent May," I tell her.

"you've gotten better too," she answers. "Agent Horton, this is Agent Skye I was wandering if you would like to join the New S.H.I.E.L.D I'm forming."

"Nice to meet you Agent Skye," I said to her.

"Do you have a first name?" Skye asks me.

"John," he says.

"Fury, told me to make sure S.H.I.E.L.D. wouldn't fall to Hydra and to protect the Earth. I would be honor to join." I hear an alarm. I go over to the computer. Agent Coulson, Agent Skye, and Agent May followed after me. I turned the computer on and entered the password. Perimeter breeched it says. Apparently my father design this to detect Hydra.

"How many are out there?" Agent Skye asks.

"No idea," I said looking into her eyes but looked away. I grab stuff that I didn't want Hydra to find.

The Necromancer along with around thirty-six Hydra soldiers and two Inhumans loyal to Hydra are with him. The Necromancer looks at the house and he has flashbacks after seeing the house. "Move in," he says. Six Hydra soldiers move towards the door. They place a breeching charge on the door. The door is breech and they toss in a flashbang. They entered the house but we left from the back door. Two Hydra soldiers spotted us but I shot them dead. The house explodes killing the twelve Hydra soldiers inside. The Inhuman walks out. He sees me and runs towards me. The Inhuman tackles me. He starts punching me in the face. Skye shoots him in the back he turns towards her getting off of me. He shoots some sort of fireball at her. She dodges the fireball. However he's on her before she could get back on her feet. He punches her knocking her unconscious as he's about to kill her I get up removing my combat knife and stick the knife into his back he turns around but I blocked his punch. He tries again but I blocked that too. Every move he tries I parry and strike with my own. He shoots a fireball at me but I freeze it from my hands. Agent Coulson and Agent May are firing at the Hydra soldiers. They manage to kill 3 more Hydra soldiers. The other two Inhumans haven't entered the fray yet one I recognized as the one I thought I killed with a knife to the back of his head but someone must have removed it I guess next time I'll have to cut off his head. I noticed the Hydra soldiers have Coulson and May pinned down. I knew I had to end this fight quickly. I grabbed him by the throat. He tried to use fire but I was turning his body cold from the inside. In only a few seconds the Inhuman was completely frozen I then hit him breaking him into pieces. Two Hydra soldiers fire at me I dodge them picking up my own pistol I shoot them both in the head. Coulson and May can't get up without being cut down by the four Hydra soldiers. The fourth and third Hydra soldiers I take out first. The third I throw a shrunken into the base of his neck. The fourth I just broke his neck which leaves just 1 and 2. I come behind two Hydra soldiers firing at Coulson and May. The first Hydra soldier I broke his neck and shot the second in the head at the same time. They get up and joined with me. The three Inhumans along with the remaing Hydra soldiers. "Coulson, Agent May, we need to get out of here?" I go over to Skye whose still unconscious and pick her up. The Hydra soldiers are getting into positions with their weapons pointing directly at us. The Necromancer steps forward.

"Drop your weapons and surrender the Inhuman and you can go free otherwise my men will kill you." I looked at him and the other 2 Inhumans. Agent Backlot draws his two SMGs. He opens fire, but everything stopped the only ones who weren't affected are us.

"What happened?" May asks.

"he froze time," Coulson replies. "Fury, was right you are special."

"We need to get out of here," I tell them. We ran for the S.H.I.E.L.D. SUV. I laid Skye gently down in the backseat. I get in the back with her while Coulson and May get into the front. Agent May hits the accelerator and we're off. A few seconds after we left they unfroze.

"What happened?" Agent Backlot asks.

"He froze time," the Necromancer says.

"He must be some Inhuman to have those powers."

"Whitehall wants him so he can harness those powers," the Necromancer replies. "Send our surviving soldiers after them." Agent Backlot nods. He turned towards the surviving Hydra soldiers.

"Get in the vehicles and catch them kill all but the Inhuman," he tells them.

"Yes sir," they reply. They move towards the vehicles. Miniguns appeared on the roofs of their SUVs. They drive after us. It took them only a few minutes to catch up to us.

"Do you have any weapons in here?" I ask them. Skye is still unconscious. I figure she must have a slight concussion or something.

"They're in the back," Coulson replies. I looked in the back and find a small stock of weapons one being an RPG and the other being a sniper rifle. I take the sniper rifle. I open the hatch to the roof. I deploy the bipod on the roof. "you'll never be able to hit them."

"I want be so sure Coulson I've seen him hit plenty of targets in different scenarios at the Academy." I made sure the armor-piercing bullets SHIELD design to go through armor vehicles are loaded into the gun. My first target are the gunners. As we go around the corner I fired. The projectile hits the soldier in the head. The second shot goes through the driver's window of the first Hydra SUV hit the driver in the face killing him instantly the vehicle drives off the road and crashes into a tree. The Second SUV fires but the armor his holding for now. I fired again but this time at the driver with the driver dead the SUV flips over at high speed and explodes. The third and last SUV is ordered to stop pursuit and wait for reinforcements before continuing. I fired a third time before they stopped pursuit killing the gunner.

"Nice shooting," Coulson says to me. "how did you hit those targets around the corner?"

"Don't know just got lucky I guess," I reply.

"How is she?" Coulson asks. I check her pulse. I touched her forehead. They didn't know it neither did I but I was healing her injuries. She awakes with her head in my lap.

"What happened and how did I get in this van?"

"You were knocked unconscious you might have a concussion you'll probably need an exam when we get back to base. I carried you to the van and put you inside."

"Thank you," she says and gives me a kiss on the cheek.

"Coulson, where are we heading I doubt SHIELD has any aircraft in the area." All of sudden Agent May stops the SUV. A ramp drop, four SHIELD Agents are inside all armed with MP5 SMGs. May drives the SUV onboard.

"Welcome to the "Bus," Coulson says. We get out of the SUV. "Agent May, get to the cockpit we may have Hydra on our ass. Head back to the Playground." The ramp closes. "Skye, why don't you introduce Agent Horton to the rest of the team."

"Follow me Agent Horton," she says. "By the way I've never got your first name."

"John," I answer. I followed her to the upperdeck of the BUS. There she introduces me to Mack and Antoine Triplett. May gets us airborne but as soon as we're in the air Hydra Quienjets are on us. They open fire but don't hit the plane. One of the Hydra pilot's attempts to contact the plane. However, Agent May doesn't answer she calls Coulson to the cockpit.

"Coulson, what are we going to do? They're threating to blow us out of the sky." I arrived at the cockpit with Skye.

"Sir I can take them out," I tell Director Coulson.

"How you plan on doing that?" Skye asks.

"I'll teleport over there and neutralize the crew. Once I have control of one of the Quienjets I can shoot the other one down and dock with the plane." Coulson nods his head in agreement.

"I'm coming with you," Skye says. I placed my arms around her waist and we teleport to the nearest Quienjet. As soon as we appeared. The three Hydra soldiers in the back turned towards us. However, they didn't have a chance to pull up their weapons. I already threw a knife at the nearest soldier. The second soldier comes at me but I kick him in the face breaking his neck. Skye neutralize the third soldier with CQC moves. The copilot gets up and its Agent Backlot.

"Skye take care of the pilot and set autopilot," I tell her.

"I don't know how to fly a Quienjet," she replies.

"no better time to learn, contact May once you neutralize the pilot I'll take care of him." agent Backlot comes at me. He picks me up but I use CQC on him to get him on the ground break his arm. Once we get onto our feet he just pops his arm back into place. He picks up a fire axe and swings it at my head but I duck just in the nick of time. I sweep the legs out from under him but he's back up in a second. He pulls out a pistol but I kick his gun out of his hand. We get in to a boxing match but he manages to get an upper hand when the Quienjet moves some. "Skye," I said.

"I'm working on it," she says. she tries to level the Quienjet out. He started to strangle me but I remove a knife and stabbed it right into his left eye. He let out a scream and pulled the knife out with the eye. However, he doesn't have time to recover before I punched him in the face. I draw another knife grabbed him. I stabbed him the back of head and he stopped struggling. I broke the knife off inside of him. I get over to the copilot seat. I take over the flying. The second Quienjets I get a missile lock on it. I hear the Hydra pilots voice on the other Quienjet before it blows up. We dock we the plane. May cloaks the plane and heads for the playground. We reenter the Bus.

"So Agent Horton are you going to join us?" I nod.

"Welcome back to the new S.H.I.E.L.D. ," he says.

 **Author Note: I hope you enjoy this chapter of Agents of S.H.I.E.L.D. War against Hydra. Please favorite, review, follow.**


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